14 research outputs found
Biallelic Variants in CTU2 Cause DREAM-PL Syndrome and Impair Thiolation of tRNA Wobble U34
No full textThe wobble position in the anticodon loop of tRNA is subject to numerous post-transcriptional modifications. In particular, thiolation of the wobble uridine has been shown to play an important role in codon-anticodon interactions. This modification is catalyzed by a highly conserved CTU1/CTU2 complex, disruption of which has been shown to cause abnormal phenotypes in yeast, worms and plants. We have previously suggested that a single founder splicing variant in human CTU2 causes a novel multiple congenital anomalies syndrome consisting of dysmorphic facies, renal agenesis, ambiguous genitalia, microcephaly, polydactyly, and lissencephaly (DREAM-PL). In this work, we describe five new patients with DREAM-PL phenotype and whose molecular analysis expands the allelic heterogeneity of the syndrome to five different alleles; four of which predict protein truncation. Functional characterization using patient-derived cells for each of these alleles, as well as the original founder allele; revealed a specific impairment of wobble uridine thiolation in all known thiol-containing tRNAs. Our data establish a recognizable CTU2-linked autosomal recessive syndrome in humans characterized by defective thiolation of the wobble uridine. The potential deleterious consequences for the translational efficiency and fidelity during development as a mechanism for pathogenicity represent an attractive target of future investigations. This article is protected by copyright. All rights reserved
A novel mechanism for variable phenotypic expressivity in Mendelian diseases uncovered by an AU-rich element (ARE)-creating mutation
No full textAbstract Background Variable expressivity is a well-known phenomenon in which patients with mutations in one gene display varying degrees of clinical severity, potentially displaying only subsets of the clinical manifestations associated with the multisystem disorder linked to the gene. This remains an incompletely understood phenomenon with proposed mechanisms ranging from allele-specific to stochastic. Results We report three consanguineous families in which an isolated ocular phenotype is linked to a novel 3′ UTR mutation in SLC4A4, a gene known to be mutated in a syndromic form of intellectual disability with renal and ocular involvement. Although SLC4A4 is normally devoid of AU-rich elements (AREs), a 3′ UTR motif that mediates post-transcriptional control of a subset of genes, the mutation we describe creates a functional ARE. We observe a marked reduction in the transcript level of SLC4A4 in patient cells. Experimental confirmation of the ARE-creating mutation is shown using a post-transcriptional reporter system that reveals consistent reduction in the mRNA-half life and reporter activity. Moreover, the neo-ARE binds and responds to the zinc finger protein ZFP36/TTP, an ARE-mRNA decay-promoting protein. Conclusions This novel mutational mechanism for a Mendelian disease expands the potential mechanisms that underlie variable phenotypic expressivity in humans to also include 3′ UTR mutations with tissue-specific pathology
A novel mechanism for variable phenotypic expressivity in Mendelian diseases uncovered by an AU-rich element (ARE)-creating mutation
No full textBreast implant-associated anaplastic large-cell lymphoma: Long-term follow-up of 60 patients
No full textPurpose: Breast implant-associated anaplastic large-cell lymphoma (ALCL) is a recently described clinicopathologic entity that usually presents as an effusion-associated fibrous capsule surrounding an implant. Less frequently, it presents as a mass. The natural history of this disease and long-term outcomes are unknown. Patients and Methods: We reviewed the literature for all published cases of breast implant-associated ALCL from 1997 to December 2012 and contacted corresponding authors to update clinical follow-up. Results: The median overall survival (OS) for 60 patients was 12 years (median follow-up, 2 years; range, 0-14 years). Capsulectomy and implant removal was performed on 56 of 60 patients (93percent). Therapeutic data were available for 55 patients: 39 patients (78percent) received systemic chemotherapy, and of the 16 patients (28percent) who did not receive chemotherapy, 12 patients opted for watchful waiting and four patients received radiation therapy alone. Thirty-nine (93percent) of 42 patients with disease confined by the fibrous capsule achieved complete remission, compared with complete remission in 13 (72percent) of 18 patients with a tumor mass. Patients with a breast mass had worse OS and progression-free survival (PFS; P = .052 and P = .03, respectively). The OS or PFS were similar between patients who received and did not receive chemotherapy (P = .44 and P = .28, respectively). Conclusion: Most patients with breast implant-associated ALCL who had disease confined within the fibrous capsule achieved complete remission. Proper management for these patients may be limited to capsulectomy and implant removal. Patients who present with a mass have a more aggressive clinical course that may be fatal, justifying cytotoxic chemotherapy in addition to removal of implants. © 2013 by American Society of Clinical Oncology.Aladily TN, 2012, AM J SURG PATHOL, V36, P1000, DOI 10.1097-PAS.0b013e31825749b1; Aladily TN, 2012, LEUKEMIA LYMPHOMA, V53, P749, DOI 10.3109-10428194.2011.639020; Alobeid B, 2009, LEUKEMIA LYMPHOMA, V50, P831, DOI 10.1080-10428190902795527; Bekkenk MW, 2000, BLOOD, V95, P3653; Bishara MRY, 2009, DIAGN PATHOL, V4, DOI 10.1186-1746-1596-4-11; Carty MJ, 2011, PLAST RECONSTR SURG, V128, p112E, DOI 10.1097-PRS.0b013e318221db96; de Jong D, 2008, JAMA-J AM MED ASSOC, V300, P2030, DOI 10.1001-jama.2008.585; Do V, 2010, AM SURGEON, V76, P1030; Farkash Evan A, 2009, J Hematop, V2, P237, DOI 10.1007-s12308-009-0043-y; GABRIEL SE, 1995, J CLIN EPIDEMIOL, V48, P527, DOI 10.1016-0895-4356(94)00209-9; Gaudet G, 2002, LEUKEMIA LYMPHOMA, V43, P115, DOI 10.1080-10428190290000392; Gualco G, 2009, APPL IMMUNOHISTO M M, V17, P301, DOI 10.1097-PAI.0b013e318195286d; Hanson Summer E, 2010, Plast Reconstr Surg, V126, p39e, DOI 10.1097-PRS.0b013e3181dab2e0; Keech JA, 1997, PLAST RECONSTR SURG, V100, P554, DOI 10.1097-00006534-199708000-00065; Lechner MG, 2011, CANCER-AM CANCER SOC, V117, P1478, DOI 10.1002-cncr.25654; Li Shiyong, 2009, Int J Clin Exp Pathol, V3, P117; Miranda RN, 2009, ARCH PATHOL LAB MED, V133, P1383, DOI 10.1043-1543-2165-133.9.1383; Newman MK, 2008, J PLAST RECONSTR AES, V61, P822, DOI 10.1016-j.bjps.2007.03.027; Olack B, 2007, ANN PLAS SURG, V59, P56, DOI 10.1097-SAP.0b013e31804d442e; Popplewell L, 2011, LEUKEMIA LYMPHOMA, V52, P1481, DOI 10.3109-10428194.2011.574755; Ralfkiaer E, 2008, PRIMARY CUTANEOUS CD, P300; Roden AC, 2008, MODERN PATHOL, V21, P455, DOI 10.1038-modpathol.3801024; Sahoo Sunati, 2003, Arch Pathol Lab Med, V127, pe115; Silverman BG, 1996, ANN INTERN MED, V124, P744; Smith TJ, 2012, BREAST, V21, P102, DOI 10.1016-j.breast.2011.07.007; Talwalkar SS, 2008, AM J SURG PATHOL, V32, P1299, DOI 10.1097-PAS.0b013e318165eb50; Taylor KO, 2012, PLAST RECONSTR SURG, V129, p610E, DOI 10.1097-PRS.0b013e3182450aae; US Food and Drug Administration, 2013, AN LARG CELL LYMPH A; US Food and Drug Administration, 2013, MED DEV COMM REP AN; Zarbo RJ, 1999, ARCH PATHOL LAB MED, V123, P1335111
Biallelic Mutations in Tetratricopeptide Repeat Domain 26 (Intraflagellar Transport 56) Cause Severe Biliary Ciliopathy in Humans
No full textAnalysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics.
No full textBACKGROUND:At least 50% of patients with suspected Mendelian disorders remain undiagnosed after whole-exome sequencing (WES), and the extent to which non-coding variants that are not captured by WES contribute to this fraction is unclear. Whole transcriptome sequencing is a promising supplement to WES, although empirical data on the contribution of RNA analysis to the diagnosis of Mendelian diseases on a large scale are scarce. RESULTS:Here, we describe our experience with transcript-deleterious variants (TDVs) based on a cohort of 5647 families with suspected Mendelian diseases. We first interrogate all families for which the respective Mendelian phenotype could be mapped to a single locus to obtain an unbiased estimate of the contribution of TDVs at 18.9%. We examine the entire cohort and find that TDVs account for 15% of all "solved" cases. We compare the results of RT-PCR to in silico prediction. Definitive results from RT-PCR are obtained from blood-derived RNA for the overwhelming majority of variants (84.1%), and only a small minority (2.6%) fail analysis on all available RNA sources (blood-, skin fibroblast-, and urine renal epithelial cells-derived), which has important implications for the clinical application of RNA-seq. We also show that RNA analysis can establish the diagnosis in 13.5% of 155 patients who had received "negative" clinical WES reports. Finally, our data suggest a role for TDVs in modulating penetrance even in otherwise highly penetrant Mendelian disorders. CONCLUSIONS:Our results provide much needed empirical data for the impending implementation of diagnostic RNA-seq in conjunction with genome sequencing.We thank the study participants for their participation. We thank the Sequencing and Genotyping Core Facilities at KFSRHC and the Bioscience Core Lab at KAUST for their technical help
Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics
No full textAbstract Background At least 50% of patients with suspected Mendelian disorders remain undiagnosed after whole-exome sequencing (WES), and the extent to which non-coding variants that are not captured by WES contribute to this fraction is unclear. Whole transcriptome sequencing is a promising supplement to WES, although empirical data on the contribution of RNA analysis to the diagnosis of Mendelian diseases on a large scale are scarce. Results Here, we describe our experience with transcript-deleterious variants (TDVs) based on a cohort of 5647 families with suspected Mendelian diseases. We first interrogate all families for which the respective Mendelian phenotype could be mapped to a single locus to obtain an unbiased estimate of the contribution of TDVs at 18.9%. We examine the entire cohort and find that TDVs account for 15% of all “solved” cases. We compare the results of RT-PCR to in silico prediction. Definitive results from RT-PCR are obtained from blood-derived RNA for the overwhelming majority of variants (84.1%), and only a small minority (2.6%) fail analysis on all available RNA sources (blood-, skin fibroblast-, and urine renal epithelial cells-derived), which has important implications for the clinical application of RNA-seq. We also show that RNA analysis can establish the diagnosis in 13.5% of 155 patients who had received “negative” clinical WES reports. Finally, our data suggest a role for TDVs in modulating penetrance even in otherwise highly penetrant Mendelian disorders. Conclusions Our results provide much needed empirical data for the impending implementation of diagnostic RNA-seq in conjunction with genome sequencing
Bi-allelic genetic variants in the translational GTPases GTPBP1 and GTPBP2 cause a distinct identical neurodevelopmental syndrome
No full text: The homologous genes GTPBP1 and GTPBP2 encode GTP-binding proteins 1 and 2, which are involved in ribosomal homeostasis. Pathogenic variants in GTPBP2 were recently shown to be an ultra-rare cause of neurodegenerative or neurodevelopmental disorders (NDDs). Until now, no human phenotype has been linked to GTPBP1. Here, we describe individuals carrying bi-allelic GTPBP1 variants that display an identical phenotype with GTPBP2 and characterize the overall spectrum of GTP-binding protein (1/2)-related disorders. In this study, 20 individuals from 16 families with distinct NDDs and syndromic facial features were investigated by whole-exome (WES) or whole-genome (WGS) sequencing. To assess the functional impact of the identified genetic variants, semi-quantitative PCR, western blot, and ribosome profiling assays were performed in fibroblasts from affected individuals. We also investigated the effect of reducing expression of CG2017, an ortholog of human GTPBP1/2, in the fruit fly Drosophila melanogaster. Individuals with bi-allelic GTPBP1 or GTPBP2 variants presented with microcephaly, profound neurodevelopmental impairment, pathognomonic craniofacial features, and ectodermal defects. Abnormal vision and/or hearing, progressive spasticity, choreoathetoid movements, refractory epilepsy, and brain atrophy were part of the core phenotype of this syndrome. Cell line studies identified a loss-of-function (LoF) impact of the disease-associated variants but no significant abnormalities on ribosome profiling. Reduced expression of CG2017 isoforms was associated with locomotor impairment in Drosophila. In conclusion, bi-allelic GTPBP1 and GTPBP2 LoF variants cause an identical, distinct neurodevelopmental syndrome. Mutant CG2017 knockout flies display motor impairment, highlighting the conserved role for GTP-binding proteins in CNS development across species
